Tweet
I was wondering if some one can point me to a commercial or open source tool to call SNPs as well Copy number variation from Illumina's sequencing data. Thanks.
Mathew
Mathew
-
-
You might want to start by looking at the software page. Also, you might get more responses if you can refine your question. -
Hi,
You can try VarScan, it's a free software, which gives SNP, indel and CNV.
Good luck,
JaneComment
-
The GenomeStudio Software package comprises seven discrete application modules that enable you to conveniently compare data from different applications.Comment
-
I have a related question: Can the copy number algorithm of VarScan still be used if my tumor and normal data are sequenced to varying depths? Lets says mean tumor depth is 2.5 times mean normal depth.. Is it still useful? If so, how should I modify the command line?Originally posted by Jane M View PostComment
-
You might be better off with specific tools for certain aspects of he jobs hat you areatte,ping to do rather than looking for a 'one tool for all jobs, approach, which as far as I'm concerned doesn't really exist!
For variant calling I would suggest looking at the Broad's V3 exome pipeline and working from there. In addition to the CNV suggestions from above, have a look at CONTRAComment
-
Kheloyaar: The Complete Guide to Kheloyaar Loginand Kheloyaar ID
The online gaming industry has transformed the way people enjoy digital entertainment. As technology continues to improve, players are looking for platforms that offer convenience, security, and a seamless user experience. Kheloyaarhas gained attention among users who value an easy-to-use platform, quick account access, and a simple registration process.
Whether you're exploring Kheloyaar for the first time or want to understand...Today, 09:27 PM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...Today, 11:10 AM -
Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...Yesterday, 05:17 AM
Comment